Merge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 963a7cf..1479d94 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
 
 import java.util.ArrayList;
 import java.util.Enumeration;
@@ -725,26 +726,13 @@ public class Sequence implements SequenceI
     {
       return;
     }
-    // TODO use StringUtils.deleteChars
 
-    char[] tmp;
-
-    if (j >= sequence.length)
-    {
-      tmp = new char[i];
-      System.arraycopy(sequence, 0, tmp, 0, i);
-      j = sequence.length;
-    }
-    else
-    {
-      tmp = new char[sequence.length - j + i];
-      System.arraycopy(sequence, 0, tmp, 0, i);
-      System.arraycopy(sequence, j, tmp, i, sequence.length - j);
-    }
+    char[] tmp = StringUtils.deleteChars(sequence, i, j);
     boolean createNewDs = false;
-    // TODO: take a look at the new dataset creation validation method below -
-    // this could become time comsuming for large sequences - consider making it
-    // more efficient
+    // TODO: take a (second look) at the dataset creation validation method for
+    // the very large sequence case
+    int eindex = -1, sindex = -1;
+    boolean ecalc = false, scalc = false;
     for (int s = i; s < j; s++)
     {
       if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
@@ -755,7 +743,11 @@ public class Sequence implements SequenceI
         }
         else
         {
-          int sindex = findIndex(start) - 1;
+          if (!scalc)
+          {
+            sindex = findIndex(start) - 1;
+            scalc = true;
+          }
           if (sindex == s)
           {
             // delete characters including start of sequence
@@ -765,7 +757,11 @@ public class Sequence implements SequenceI
           else
           {
             // delete characters after start.
-            int eindex = findIndex(end) - 1;
+            if (!ecalc)
+            {
+              eindex = findIndex(end) - 1;
+              ecalc = true;
+            }
             if (eindex < j)
             {
               // delete characters at end of sequence